Structure of PDB 8ppt Chain A

Receptor sequence
>8pptA (length=447) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence]
EYSKYEDVVIEWNPSVTPVQIEKNYEVKFDVRQVKLRPPKVKNGSGKEGE
IIVEAYASLFKSRLSKLKRILRENPEISNVVDIGKLNYVSGDEEVTIIGL
VNSKRETNRGLIFEVEDKTGIVKVFLPKDSEDYREAFKVLPDAVVAFKGF
YSKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKA
FLKFLEWLNGHVESKEEEEIVSRVKYLIIAGDVVDGIGIYPGQYSDLVIP
DIFDQYEALANLLANVPEHITMFIGPGNADAARPAIPQPEFYKEYAKPIY
KLKNAIIISNPAVIRLHGRDFLIAHGRGIEDVVSFVPGLTHHKPGLPMVE
LLKMRHLAPTFGGKVPIAPDPEDLLVIEEVPDLVQMGHVHVYDAVVYRGV
QLVNSATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC
3D structure
PDB8ppt Molecular basis for proof-reading by Family-D DNA polymerases
ChainA
Resolution2.9 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.1: exodeoxyribonuclease I.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna A I411 Y412 E502 H560 V561 F586 I592 I239 Y240 E330 H388 V389 F414 I420
BS02 MG A D404 N450 H497 H560 D232 N278 H325 H388
BS03 MG A D360 D404 D188 D232
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0004527 exonuclease activity
GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
GO:0008408 3'-5' exonuclease activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006308 DNA catabolic process
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0042575 DNA polymerase complex

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Molecular Function
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Cellular Component
External links
PDB RCSB:8ppt, PDBe:8ppt, PDBj:8ppt
PDBsum8ppt
PubMed38097591
UniProtQ9V2F3|DP2S_PYRAB DNA polymerase II small subunit (Gene Name=polB)

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